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design matrix
•
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18
votes
37
replies
17k
views
Correct construction of design matrix in limma for multiple contrasts for gene expression profiling
limma
illumina
differential gene expression
multiple comparisons
design matrix
8.9 years ago • updated 8.8 years ago
svlachavas
▴ 830
2
votes
4
replies
8.5k
views
Limma LmFit() giving error: Error in lm.fit(design, t(M)) : incompatible dimension
limma
differential expression
design matrix
error
eset
updated 8.8 years ago by
Aaron Lun
★ 28k • written 8.8 years ago by
Vani
▴ 20
0
votes
1
reply
7.8k
views
DESeq2: how to construct the design matrix?
deseq2
design matrix
limma design matrix
updated 9.0 years ago by
Michael Love
42k • written 9.0 years ago by
taf
• 0
1
vote
2
replies
7.5k
views
DESEQ2 design with multiple conditions
deseq2
design matrix
updated 6.0 years ago by
Michael Love
42k • written 6.0 years ago by
vrehaman
• 0
6
votes
3
replies
6.9k
views
deseq2 correcting for batch effects
deseq2
batch effect
removebatcheffect()
design matrix
updated 6.6 years ago by
Michael Love
42k • written 6.6 years ago by
Assa Yeroslaviz
★ 1.5k
3
votes
4
replies
4.9k
views
multiple comparison using limma
limma
design matrix
makecontrasts
multiple comparisons
7.3 years ago • updated 7.2 years ago
annabelle.congras
▴ 10
11
votes
14
replies
4.3k
views
Setting up the Design Matrix
rnaseq
edgeR
multiple factor design
design matrix
8.3 years ago
Yogender Gowtham
▴ 20
0
votes
8
replies
3.9k
views
Design question limma multi variables
limma
design matrix
updated 7.3 years ago by
Aaron Lun
★ 28k • written 7.3 years ago by
Stane
▴ 40
2
votes
5
replies
3.8k
views
design model matrix for nested factors (edgeR)
edger
design matrix
model matrix
updated 9.1 years ago by
Aaron Lun
★ 28k • written 9.1 years ago by
silvia.paolucci81
• 0
2
votes
8
replies
3.7k
views
EdgeR. Analysis with pairing across condition and treatment. Design Matrix
edger
ANOVA
Design matrix
updated 9.3 years ago by
Gordon Smyth
50k • written 9.3 years ago by
chwhite
• 0
5
votes
7
replies
3.6k
views
Deseq2 design for one condition over 8 different time point
deseq2
rna-seq
design matrix
deseq
updated 5.6 years ago by
Michael Love
42k • written 5.6 years ago by
thindmarsmission
▴ 10
2
votes
6
replies
3.3k
views
RNA-seq paired analysis design
paired samples
design matrix
limma
deseq2
edger
updated 7.3 years ago by
Gordon Smyth
50k • written 7.3 years ago by
cjmb3
• 0
7
votes
11
replies
3.3k
views
Continuous variable interaction with Groups in design matrix
edger
design matrix
updated 8.3 years ago by
Aaron Lun
★ 28k • written 8.3 years ago by
jhj89
▴ 10
0
votes
11
replies
3.2k
views
Limma Design Matrix for Paired Samples with Confouding Factors
limma
design matrix
paired samples
confounding factors
updated 5.5 years ago by
Aaron Lun
★ 28k • written 5.5 years ago by
yuabrahamliu
• 0
0
votes
2
replies
3.0k
views
Time-course analysis with limma for >3 time points
limma
contrast matrix
design matrix
multiple time points
timecourse
updated 3.0 years ago by
rf
• 0 • written 6.9 years ago by
relathman
▴ 20
2
votes
10
replies
2.8k
views
Time-series analysis with DESeq2
deseq2
time-series
design matrix
edger
updated 5.2 years ago by
Michael Love
42k • written 5.2 years ago by
Assa Yeroslaviz
★ 1.5k
3
votes
12
replies
2.8k
views
Questions about complex design in limma regarding an agilent microarray dataset with multiple time points and different biological replicates
limma
design matrix
multiple time points
agilent microarrays
updated 8.2 years ago by
Aaron Lun
★ 28k • written 8.2 years ago by
Konstantinos Yeles
▴ 80
6
votes
4
replies
2.6k
views
discrepance in DESeq2 results with different design structures
deseq2
differential expression
independent filtering
pre-filtering
design matrix
9.0 years ago
Assa Yeroslaviz
★ 1.5k
4
votes
8
replies
2.5k
views
Can't find any differentially expressed genes
rnaseq
differential gene expression
design matrix
edgeR
updated 9.1 years ago by
Gordon Smyth
50k • written 9.1 years ago by
s3462450
▴ 10
1
vote
1
reply
2.5k
views
EdgeR:Calculating differential expression within/between groups in nested designs
edger
nested
design matrix
differential expression
updated 9.2 years ago by
Aaron Lun
★ 28k • written 9.2 years ago by
Mauve
• 0
2
votes
2
replies
2.4k
views
DMRcate cpg.annotate error
dmrcate
design matrix
updated 8.5 years ago by
Tim Peters
▴ 180 • written 8.5 years ago by
Giovanni Calice
▴ 160
0
votes
7
replies
2.4k
views
DESeq2: how to identify confounding variable in the design matrix
deseq2
confounders
design matrix
rnaseq
7.0 years ago
lina.faller
▴ 10
0
votes
1
reply
2.2k
views
EdgeR: setting reference condition and design matrix headers
edgeR
reference
design matrix
multiple factor design
updated 8.9 years ago by
Aaron Lun
★ 28k • written 8.9 years ago by
Ekarl2
▴ 80
2
votes
13
replies
2.1k
views
LIMMA : group specific effect of a treatment while controlling for individual effect
limma-voom
design matrix
limma time-course
limma design matrix
limma
6.2 years ago
SPbeginner
• 0
2
votes
10
replies
2.1k
views
Design matrix for unbalanced data
edgeR
RNA-Seq
design matrix
multifactorial design
8.2 years ago
Yogender Gowtham
▴ 20
5
votes
12
replies
2.0k
views
how to use edgeR analysis RNA-seq data which has four factors
edger
design matrix
comparing more than two groups
multiple factor design
8.3 years ago • updated 8.1 years ago
xiaoaozqd
• 0
1
vote
18
replies
2.0k
views
Microarray expression analysis for on factor taking account confounders (covariables)
limma
design matrix
matrix with covariables
updated 6.2 years ago by
Aaron Lun
★ 28k • written 6.2 years ago by
michel655
• 0
3
votes
7
replies
2.0k
views
complex design for chip-seq analysis
chipseq
csaw
limma
design matrix
multiple factor design
updated 6.5 years ago by
Aaron Lun
★ 28k • written 6.5 years ago by
Assa Yeroslaviz
★ 1.5k
2
votes
13
replies
1.9k
views
problem about (design matrix)
limma
limma design matrix
design matrix
updated 8.2 years ago by
Aaron Lun
★ 28k • written 8.2 years ago by
libya.tahani
• 0
5
votes
2
replies
1.9k
views
DESeq2 batch effect with and without interaction model
deseq2
rna-seq
R
linear model
design matrix
updated 6.5 years ago by
Michael Love
42k • written 6.5 years ago by
gdagstn
▴ 10
2
votes
10
replies
1.8k
views
Am I on the right tracks with a 3 factor design in Limma?
r
limma
design matrix
biobase
updated 5.8 years ago by
Gordon Smyth
50k • written 5.8 years ago by
reubenmcgregor88
• 0
1
vote
17
replies
1.8k
views
design for edgeR
edger
design matrix
glmlrt
updated 7.4 years ago by
Aaron Lun
★ 28k • written 7.4 years ago by
simarsidhu25
• 0
4
votes
4
replies
1.7k
views
Is this design matrix correct (treament factor with three levels)?
edger
limma
design matrix
8.2 years ago
Ekarl2
▴ 80
4
votes
4
replies
1.7k
views
edgeR: How can I determine which factors significantly explain my DE genes?
edger
differential gene expression
model.matrix
design matrix
updated 6.0 years ago by
Gordon Smyth
50k • written 6.0 years ago by
Robert Gilmore
• 0
0
votes
5
replies
1.7k
views
DESeq2 package : Error in checkFullRank(modelMatrix) while designing multi factor
DESeq2
multiple factor design
design model
design matrix
rna-seq
updated 5.4 years ago by
Michael Love
42k • written 5.4 years ago by
iammiso
• 0
3
votes
6
replies
1.7k
views
Design that evaluates response to continuous and categorical variables
limma
design and contrast matrix
design matrix
limma design matrix
updated 8.9 years ago by
James W. MacDonald
65k • written 8.9 years ago by
Moritz E. Beber
▴ 10
1
vote
8
replies
1.6k
views
Design matrix for regressing gene expression on a continuous variable - age
limma
lmfit
design matrix
r
updated 5.8 years ago by
Aaron Lun
★ 28k • written 5.8 years ago by
anupriya.dalmia
• 0
2
votes
1
reply
1.6k
views
using variable in design formula
deseq2
r
design matrix
updated 7.7 years ago by
Michael Love
42k • written 7.7 years ago by
igor
▴ 40
0
votes
4
replies
1.6k
views
edgeR design matrix
edgeR
design and contrast matrix
design matrix
updated 6.1 years ago by
Gordon Smyth
50k • written 6.2 years ago by
cafelumiere12
▴ 20
7
votes
5
replies
1.6k
views
Which is the best design matrix to compare a timecourse between two conditions?
limma
voom
design matrix
timecourse
updated 7.3 years ago by
Gordon Smyth
50k • written 7.3 years ago by
Camila Orellana
▴ 10
3
votes
7
replies
1.6k
views
single continuous factor
edger
design matrix
continuous
updated 2.2 years ago by
Tongjun
• 0 • written 6.0 years ago by
ashley.lu
• 0
1
vote
4
replies
1.6k
views
edgeR design matrix for 2 variables + batch effect
egdeR
design matrix
batch effect
updated 4.5 years ago by
Gordon Smyth
50k • written 4.5 years ago by
ahsindoomilup
• 0
0
votes
2
replies
1.5k
views
stimulation effects between wild-type and knockout cells using deseq
multiple factor design
interactions
design matrix
deseq2
updated 6.5 years ago by
Michael Love
42k • written 8.5 years ago by
Assa Yeroslaviz
★ 1.5k
5
votes
5
replies
1.4k
views
Design and Contrast Matrix for Linear Model. To Combine or not to Combine?
limma
design and contrast matrix
design matrix
contrast matrix
updated 5.6 years ago by
James W. MacDonald
65k • written 5.6 years ago by
mikhael.manurung
▴ 270
2
votes
2
replies
1.3k
views
EdgeR User Guide: use of glmLRT vs glmQLF in oral carcinoma Case Study
edger
design matrix
glmlrt()
glmQFTest()
paired design
5.5 years ago
oakhamwolf
• 0
3
votes
8
replies
1.3k
views
Design matrix for a two-color experimental design testing for time effect on 3 treated cell-lines, each with its own time=0 control
limma
microarray
design matrix
twochannel
updated 5.8 years ago by
Gordon Smyth
50k • written 5.8 years ago by
rubi
▴ 110
0
votes
1
reply
1.3k
views
Test for differential variability with missMethyl (DiffVar) using block design
missmethyl
diffvar
design matrix
limma
block
updated 6.0 years ago by
lhuang7
▴ 50 • written 6.9 years ago by
Simone
▴ 190
2
votes
2
replies
1.3k
views
DESeq2 multifactorial design with unpaired individuals
deseq2
design matrix
updated 7.3 years ago by
Michael Love
42k • written 7.3 years ago by
fanli.gcb
• 0
3
votes
6
replies
1.3k
views
EdgeR model formula design matrix
edger
design matrix
paired samples
updated 6.1 years ago by
Aaron Lun
★ 28k • written 6.1 years ago by
aiko
• 0
4
votes
3
replies
1.3k
views
What is the correct contrast matrix if one treatment must be compared to both of the other two treatments, but separately?
edger
limma
model.matrix
contrast matrix
design matrix
updated 7.8 years ago by
Gavin Kelly
▴ 680 • written 7.8 years ago by
Peter
• 0
50 results • Page
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Comment: Cannot connect to ExperimentHub server
by
Jiayu
• 0
Many thanks and it also resolved the same issue for me!
Comment: Help with running egsea()
by
Chris
• 0
I tried egsea.ma and got this error: gsa = egsea.ma(numeric_matrix, vector_group, probe_annotation, contrasts = contrast_matrix, gs.an…
Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
angelathuynh5
• 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
by
James W. MacDonald
65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Answer: Cannot connect to ExperimentHub server
Answer: confused with tximport counts abundance using salmon input
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
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